RNA-seq analysis forVishal group at Longwood.

Contact Lorena Pantano (lpantano@hsph.harvard.edu) for additional details.

The most recent update of this html document occurred: Mon May 23 17:31:32 2016

The sections below provide code to reproduce the included results and plots.

Overview

2016-05-23 16:47:20 INFO::Using gene counts calculated from the Sailfish transcript counts.

Quality control metrics

Mapped reads

Genomic mapping rate

Number of genes detected

Gene detection saturation

Exonic mapping rate

rRNA|mitRNA mapping rate

Estimated fragment length of paired-end reads

Boxplot of log10 counts per gene

Boxplot of log10 TMM-normalized counts per gene

Trimmed mean of M-values (TMM) normalization is described here

Robinson, M. D., & Oshlack, A. (2010). A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biology, 11(3). doi:10.1186/gb-2010-11-3-r25

Density of log10 TMM-normalized counts

Correlation (Spearman) heatmap of TMM-normalized counts

MDS plot

MDS after variation removal

We used RUVSeq package for this with two factors to explain the unwanted variation.

Differential expression

Effect of variance stabilization

Dispersion estimates

Comparison: fa_model


out of 29943 with nonzero total read count
adjusted p-value < 0.1
LFC > 0 (up) : 3185, 11%
LFC < 0 (down) : 3326, 11%
outliers [1] : 468, 1.6%
low counts [2] : 7996, 27%
(mean count < 2)
[1] see ‘cooksCutoff’ argument of ?results
[2] see ‘independentFiltering’ argument of ?results

NULL

Differential expression file at: fa_model.tsv

Normalized counts matrix file at: fa_model_log2_counts.tsv

MA plot plot

Volcano plot

QC for DE genes p-values/variance

Most significand, FDR< 0.01 and log2FC > 3 : 1024

Plots most significand

Plot top 9 genes

Top DE genes

baseMean log2FoldChange lfcSE stat pvalue padj symbol description day14vscontrol day1vscontrol day2vscontrol day3vscontrol day7vscontrol absMaxLog2FC
ENSMUSG00000040405 16311.0902 1.2719380 0.3326644 477.9036 0 0 Havcr1 hepatitis A virus cellular receptor 1 1.2719380 6.9619885 5.793616 4.7710459 3.4953820 6.961989
ENSMUSG00000028017 2685.7105 -0.7611039 0.4579820 285.1583 0 0 Egf epidermal growth factor -0.7611039 -6.4691406 -7.250125 -3.7313804 -2.3649677 7.250125
ENSMUSG00000034810 113.2406 2.0116777 0.3500331 229.7995 0 0 Scn7a sodium channel, voltage-gated, type VII, alpha 2.0116777 -2.3141228 -3.457986 0.2384421 1.3554646 3.457986
ENSMUSG00000027199 5005.4187 -1.5908413 0.4126514 220.4895 0 0 Gatm glycine amidinotransferase (L-arginine:glycine amidinotransferase) -1.5908413 -5.2620713 -4.538672 -3.5990810 -2.8571068 5.262071
ENSMUSG00000026348 765.4457 -1.4919020 0.2984488 214.3869 0 0 Acmsd amino carboxymuconate semialdehyde decarboxylase -1.4919020 -4.0416947 -2.666851 -2.6443023 -2.2875425 4.041695
ENSMUSG00000022037 8324.4031 2.2479713 0.3298258 210.9215 0 0 Clu clusterin 2.2479713 3.9511690 5.004188 4.2887266 3.2508579 5.004188
ENSMUSG00000029304 219108.8212 3.3383981 0.4638694 203.0990 0 0 Spp1 secreted phosphoprotein 1 3.3383981 6.8407038 7.447928 5.9425678 5.1756161 7.447928
ENSMUSG00000041052 2823.5800 -1.0698716 0.4527684 198.4246 0 0 Slc7a13 solute carrier family 7, (cationic amino acid transporter, y+ system) member 13 -1.0698716 -5.1809340 -5.105784 -3.1397970 -3.2483012 5.180934
ENSMUSG00000021490 10003.5172 -0.8005353 0.3195153 196.5071 0 0 Slc34a1 solute carrier family 34 (sodium phosphate), member 1 -0.8005353 -4.1142246 -3.237309 -1.7122298 -1.8162714 4.114225
ENSMUSG00000021477 5669.9734 0.9868310 0.2445081 195.7993 0 0 Ctsl cathepsin L 0.9868310 3.0552194 2.494315 2.0127698 1.1257107 3.055219
ENSMUSG00000039997 716.2957 0.0861251 0.2558293 182.6815 0 0 Ifi203 interferon activated gene 203 0.0861251 -2.3753208 -2.284695 -0.5596117 0.3729947 2.375321
ENSMUSG00000036594 1764.9060 2.4493882 0.3789872 180.5537 0 0 H2-Aa histocompatibility 2, class II antigen A, alpha 2.4493882 -1.5734717 -1.127157 1.3145226 2.4167275 2.449388
ENSMUSG00000083863 183.8333 -2.8207520 0.3095867 178.8778 0 0 NA NA -2.8207520 -2.1878619 -2.097094 -3.3755878 -2.5682524 3.375588
ENSMUSG00000004730 110.4004 2.8857456 0.5022537 178.3086 0 0 Adgre1 adhesion G protein-coupled receptor E1 2.8857456 -1.3894795 -2.255088 2.0880200 3.7236469 3.723647
ENSMUSG00000061947 379.7477 4.2422088 0.5163896 178.0911 0 0 Serpina10 serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10 4.2422088 6.3882789 6.370973 6.3176621 5.5438450 6.388279
ENSMUSG00000026365 3081.0764 2.0580137 0.3629814 176.1463 0 0 Cfh complement component factor h 2.0580137 -1.3936267 -1.926189 -0.1759390 1.6148495 2.058014
ENSMUSG00000022445 268.3951 -0.9733166 0.4565228 175.7693 0 0 Cyp2d26 cytochrome P450, family 2, subfamily d, polypeptide 26 -0.9733166 -5.2160295 -5.364363 -3.0398488 -1.7129063 5.364363
ENSMUSG00000027962 1669.8257 5.3771941 0.4724509 171.2956 0 0 Vcam1 vascular cell adhesion molecule 1 5.3771941 3.9804218 5.191675 7.0552413 6.0363334 7.055241
ENSMUSG00000083563 949.2445 -2.8970301 0.3312405 168.1643 0 0 NA NA -2.8970301 -2.4546197 -2.361608 -3.3401756 -2.7664567 3.340176
ENSMUSG00000038608 486.6631 3.1258137 0.3777503 166.7087 0 0 Dock10 dedicator of cytokinesis 10 3.1258137 0.1452071 1.155319 3.4243127 3.4959390 3.495939

GO ontology of DE genes (log2FC > 3 and FDR < 0.01 ):

ID Description GeneRatio BgRatio pvalue p.adjust qvalue
GO:0030593 GO:0030593 neutrophil chemotaxis 22/790 81/23276 0.0000000 0.0000000 0.0000000
GO:0097529 GO:0097529 myeloid leukocyte migration 29/790 152/23276 0.0000000 0.0000000 0.0000000
GO:0002685 GO:0002685 regulation of leukocyte migration 28/790 155/23276 0.0000000 0.0000000 0.0000000
GO:0050920 GO:0050920 regulation of chemotaxis 27/790 181/23276 0.0000000 0.0000000 0.0000000
GO:0050729 GO:0050729 positive regulation of inflammatory response 20/790 109/23276 0.0000000 0.0000001 0.0000001
GO:0022409 GO:0022409 positive regulation of cell-cell adhesion 27/790 201/23276 0.0000000 0.0000002 0.0000001
GO:1903036 GO:1903036 positive regulation of response to wounding 23/790 158/23276 0.0000000 0.0000004 0.0000003
GO:0002696 GO:0002696 positive regulation of leukocyte activation 30/790 278/23276 0.0000000 0.0000021 0.0000016
GO:0002526 GO:0002526 acute inflammatory response 18/790 111/23276 0.0000000 0.0000026 0.0000020
GO:0070372 GO:0070372 regulation of ERK1 and ERK2 cascade 27/790 239/23276 0.0000001 0.0000035 0.0000027
GO:0050863 GO:0050863 regulation of T cell activation 28/790 257/23276 0.0000001 0.0000042 0.0000031
GO:0071347 GO:0071347 cellular response to interleukin-1 13/790 61/23276 0.0000001 0.0000067 0.0000050
GO:1902042 GO:1902042 negative regulation of extrinsic apoptotic signaling pathway via death domain receptors 9/790 26/23276 0.0000001 0.0000067 0.0000050
GO:0006959 GO:0006959 humoral immune response 22/790 175/23276 0.0000001 0.0000080 0.0000060
GO:0045765 GO:0045765 regulation of angiogenesis 25/790 221/23276 0.0000002 0.0000090 0.0000067
GO:0070661 GO:0070661 leukocyte proliferation 30/790 301/23276 0.0000002 0.0000090 0.0000067
GO:0007162 GO:0007162 negative regulation of cell adhesion 25/790 230/23276 0.0000003 0.0000177 0.0000132
GO:0032963 GO:0032963 collagen metabolic process 14/790 78/23276 0.0000003 0.0000177 0.0000132
GO:0019221 GO:0019221 cytokine-mediated signaling pathway 30/790 314/23276 0.0000004 0.0000203 0.0000152
GO:0002460 GO:0002460 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains 26/790 252/23276 0.0000005 0.0000272 0.0000204
GO:0002274 GO:0002274 myeloid leukocyte activation 20/790 162/23276 0.0000007 0.0000332 0.0000249
GO:0007596 GO:0007596 blood coagulation 20/790 173/23276 0.0000019 0.0000845 0.0000633
GO:0097191 GO:0097191 extrinsic apoptotic signaling pathway 23/790 228/23276 0.0000035 0.0001426 0.0001069
GO:0032102 GO:0032102 negative regulation of response to external stimulus 26/790 280/23276 0.0000038 0.0001518 0.0001138
GO:0031639 GO:0031639 plasminogen activation 7/790 21/23276 0.0000039 0.0001518 0.0001138
GO:0015711 GO:0015711 organic anion transport 30/790 354/23276 0.0000046 0.0001770 0.0001326
GO:0045807 GO:0045807 positive regulation of endocytosis 16/790 128/23276 0.0000072 0.0002676 0.0002006
GO:0016053 GO:0016053 organic acid biosynthetic process 24/790 256/23276 0.0000076 0.0002784 0.0002087
GO:0071346 GO:0071346 cellular response to interferon-gamma 11/790 63/23276 0.0000079 0.0002838 0.0002127
GO:0050679 GO:0050679 positive regulation of epithelial cell proliferation 18/790 161/23276 0.0000096 0.0003378 0.0002532
GO:0030198 GO:0030198 extracellular matrix organization 21/790 210/23276 0.0000105 0.0003633 0.0002724
GO:0034113 GO:0034113 heterotypic cell-cell adhesion 9/790 43/23276 0.0000114 0.0003908 0.0002930
GO:0050678 GO:0050678 regulation of epithelial cell proliferation 26/790 301/23276 0.0000140 0.0004648 0.0003484
GO:0010810 GO:0010810 regulation of cell-substrate adhesion 18/790 167/23276 0.0000160 0.0005220 0.0003913
GO:0002224 GO:0002224 toll-like receptor signaling pathway 12/790 82/23276 0.0000201 0.0006338 0.0004751
GO:0042063 GO:0042063 gliogenesis 23/790 259/23276 0.0000280 0.0008432 0.0006321
GO:0050708 GO:0050708 regulation of protein secretion 30/790 391/23276 0.0000313 0.0009257 0.0006939
GO:0045840 GO:0045840 positive regulation of mitotic nuclear division 9/790 53/23276 0.0000663 0.0016713 0.0012528
GO:0050878 GO:0050878 regulation of body fluid levels 25/790 311/23276 0.0000667 0.0016723 0.0012536
GO:0030336 GO:0030336 negative regulation of cell migration 19/790 203/23276 0.0000674 0.0016794 0.0012589
GO:0019886 GO:0019886 antigen processing and presentation of exogenous peptide antigen via MHC class II 5/790 14/23276 0.0000690 0.0016944 0.0012701
GO:0060740 GO:0060740 prostate gland epithelium morphogenesis 7/790 33/23276 0.0000998 0.0022718 0.0017030
GO:0007067 GO:0007067 mitotic nuclear division 29/790 399/23276 0.0001101 0.0024721 0.0018531
GO:0044275 GO:0044275 cellular carbohydrate catabolic process 9/790 58/23276 0.0001370 0.0027981 0.0020975
GO:0048771 GO:0048771 tissue remodeling 16/790 163/23276 0.0001426 0.0028587 0.0021429
GO:0009072 GO:0009072 aromatic amino acid family metabolic process 6/790 25/23276 0.0001528 0.0030176 0.0022620
GO:0016485 GO:0016485 protein processing 22/790 275/23276 0.0001915 0.0036200 0.0027136
GO:0035239 GO:0035239 tube morphogenesis 28/790 393/23276 0.0002001 0.0037178 0.0027869
GO:0010038 GO:0010038 response to metal ion 18/790 204/23276 0.0002181 0.0039848 0.0029871
GO:0045786 GO:0045786 negative regulation of cell cycle 26/790 359/23276 0.0002588 0.0046292 0.0034701
GO:1901605 GO:1901605 alpha-amino acid metabolic process 18/790 211/23276 0.0003299 0.0057347 0.0042988
GO:0090068 GO:0090068 positive regulation of cell cycle process 17/790 199/23276 0.0004701 0.0074424 0.0055789
GO:0009914 GO:0009914 hormone transport 24/790 333/23276 0.0004713 0.0074424 0.0055789
GO:0071900 GO:0071900 regulation of protein serine/threonine kinase activity 27/790 394/23276 0.0004745 0.0074660 0.0055966
GO:0010466 GO:0010466 negative regulation of peptidase activity 18/790 220/23276 0.0005443 0.0083202 0.0062369
GO:0002697 GO:0002697 regulation of immune effector process 27/790 398/23276 0.0005540 0.0084387 0.0063258
GO:0000768 GO:0000768 syncytium formation by plasma membrane fusion 8/790 56/23276 0.0005711 0.0085820 0.0064332
GO:0042742 GO:0042742 defense response to bacterium 20/790 262/23276 0.0006678 0.0096927 0.0072658
GO:0006875 GO:0006875 cellular metal ion homeostasis 29/790 445/23276 0.0006703 0.0096976 0.0072694

Clustering in common patterns

We used diana function inside cluster R package to separate genes using the expression correlation with time. Clusters with more than 20 genes are shown. A GO and KEGG enrichment is done for each group.

A summary of diana function is copied here:

The diana-algorithm constructs a hierarchy of clusterings, starting with one large cluster containing all n observations. Clusters are divided until each cluster contains only a single observation.
At each stage, the cluster with the largest diameter is selected. (The diameter of a cluster is the largest dissimilarity between any two of its observations.)
To divide the selected cluster, the algorithm first looks for its most disparate observation (i.e., which has the largest average dissimilarity to the other observations of the selected cluster). This observation initiates the "splinter group". In subsequent steps, the algorithm reassigns observations that are closer to the "splinter group" than to the "old party". The result is a division of the selected cluster into two new clusters.

Working with 1024 genes.

Working with 1024 genes

Working with 1024 genes.

group: 1

ID Description GeneRatio BgRatio pvalue p.adjust qvalue
mmu04110 mmu04110 NA 8/48 128/6698 2.8e-06 0.0002128 0.0002031
ID Description GeneRatio BgRatio pvalue p.adjust qvalue
GO:1902042 GO:1902042 negative regulation of extrinsic apoptotic signaling pathway via death domain receptors 6/118 26/23276 0.0000000 0.0000066 0.0000053
GO:0097191 GO:0097191 extrinsic apoptotic signaling pathway 11/118 228/23276 0.0000000 0.0000250 0.0000200
GO:2001233 GO:2001233 regulation of apoptotic signaling pathway 13/118 370/23276 0.0000001 0.0000362 0.0000290
GO:1903034 GO:1903034 regulation of response to wounding 13/118 394/23276 0.0000001 0.0000411 0.0000329
GO:0001525 GO:0001525 angiogenesis 12/118 424/23276 0.0000017 0.0004483 0.0003584
GO:0006270 GO:0006270 DNA replication initiation 4/118 25/23276 0.0000073 0.0012032 0.0009618
GO:0016485 GO:0016485 protein processing 9/118 275/23276 0.0000114 0.0015990 0.0012782
GO:0052547 GO:0052547 regulation of peptidase activity 10/118 352/23276 0.0000126 0.0016550 0.0013230
GO:0008630 GO:0008630 intrinsic apoptotic signaling pathway in response to DNA damage 6/118 105/23276 0.0000160 0.0019626 0.0015689
GO:1903532 GO:1903532 positive regulation of secretion by cell 10/118 389/23276 0.0000297 0.0028315 0.0022635
GO:0045786 GO:0045786 negative regulation of cell cycle 9/118 359/23276 0.0000913 0.0063758 0.0050968
GO:0031589 GO:0031589 cell-substrate adhesion 8/118 284/23276 0.0001022 0.0066892 0.0053473
GO:0042310 GO:0042310 vasoconstriction 5/118 93/23276 0.0001120 0.0071089 0.0056828
GO:0010564 GO:0010564 regulation of cell cycle process 10/118 467/23276 0.0001356 0.0083564 0.0066801

group: 2

ID Description GeneRatio BgRatio pvalue p.adjust qvalue
mmu00380 mmu00380 NA 5/59 45/6698 0.0000416 0.0032068 0.0028934
mmu04146 mmu04146 NA 5/59 80/6698 0.0006478 0.0249400 0.0225022
mmu00330 mmu00330 NA 4/59 54/6698 0.0012369 0.0317478 0.0286446
ID Description GeneRatio BgRatio pvalue p.adjust qvalue
GO:1901605 GO:1901605 alpha-amino acid metabolic process 12/132 211/23276 0.0000000 0.0000030 0.0000027
GO:0044282 GO:0044282 small molecule catabolic process 10/132 245/23276 0.0000014 0.0002529 0.0002274
GO:0006732 GO:0006732 coenzyme metabolic process 10/132 273/23276 0.0000037 0.0005824 0.0005236
GO:1990267 GO:1990267 response to transition metal nanoparticle 6/132 78/23276 0.0000055 0.0007606 0.0006839
GO:0044283 GO:0044283 small molecule biosynthetic process 12/132 448/23276 0.0000097 0.0010140 0.0009118
GO:0019369 GO:0019369 arachidonic acid metabolic process 5/132 63/23276 0.0000294 0.0024557 0.0022080
GO:0009308 GO:0009308 amine metabolic process 6/132 124/23276 0.0000767 0.0044173 0.0039717
GO:0046128 GO:0046128 purine ribonucleoside metabolic process 8/132 255/23276 0.0001064 0.0053398 0.0048012
GO:0044262 GO:0044262 cellular carbohydrate metabolic process 8/132 263/23276 0.0001316 0.0061168 0.0054998
GO:0042537 GO:0042537 benzene-containing compound metabolic process 3/132 20/23276 0.0001894 0.0074307 0.0066812
GO:0005976 GO:0005976 polysaccharide metabolic process 5/132 96/23276 0.0002198 0.0081145 0.0072961

group: 3

ID Description GeneRatio BgRatio pvalue p.adjust qvalue
mmu05150 mmu05150 NA 5/38 51/6698 0.0000087 0.0006697 0.0005493
mmu04145 mmu04145 NA 6/38 179/6698 0.0004540 0.0149832 0.0122897
mmu04650 mmu04650 NA 5/38 125/6698 0.0006402 0.0149832 0.0122897
mmu04610 mmu04610 NA 4/38 76/6698 0.0008435 0.0149832 0.0122897
mmu05020 mmu05020 NA 3/38 35/6698 0.0009729 0.0149832 0.0122897
ID Description GeneRatio BgRatio pvalue p.adjust qvalue
GO:0031349 GO:0031349 positive regulation of defense response 12/88 271/23276 0.0000000 0.0000007 0.0000005
GO:0030593 GO:0030593 neutrophil chemotaxis 8/88 81/23276 0.0000000 0.0000007 0.0000005
GO:0006935 GO:0006935 chemotaxis 14/88 491/23276 0.0000000 0.0000014 0.0000010
GO:0050778 GO:0050778 positive regulation of immune response 13/88 444/23276 0.0000000 0.0000018 0.0000013
GO:1903034 GO:1903034 regulation of response to wounding 12/88 394/23276 0.0000000 0.0000038 0.0000028
GO:0042060 GO:0042060 wound healing 11/88 326/23276 0.0000000 0.0000050 0.0000036
GO:0002250 GO:0002250 adaptive immune response 11/88 372/23276 0.0000002 0.0000149 0.0000108
GO:0006897 GO:0006897 endocytosis 12/88 495/23276 0.0000004 0.0000314 0.0000228
GO:0001819 GO:0001819 positive regulation of cytokine production 10/88 357/23276 0.0000010 0.0000835 0.0000607
GO:0002274 GO:0002274 myeloid leukocyte activation 7/88 162/23276 0.0000027 0.0002207 0.0001604
GO:0032963 GO:0032963 collagen metabolic process 5/88 78/23276 0.0000117 0.0007128 0.0005181
GO:0060840 GO:0060840 artery development 5/88 88/23276 0.0000211 0.0010953 0.0007961
GO:0050829 GO:0050829 defense response to Gram-negative bacterium 4/88 47/23276 0.0000300 0.0014197 0.0010318
GO:2000147 GO:2000147 positive regulation of cell motility 9/88 428/23276 0.0000350 0.0015858 0.0011525
GO:0071345 GO:0071345 cellular response to cytokine stimulus 9/88 450/23276 0.0000516 0.0019815 0.0014401
GO:0030198 GO:0030198 extracellular matrix organization 6/88 210/23276 0.0001471 0.0039379 0.0028620
GO:0050878 GO:0050878 regulation of body fluid levels 7/88 311/23276 0.0001789 0.0045156 0.0032818
GO:0001525 GO:0001525 angiogenesis 8/88 424/23276 0.0002045 0.0049508 0.0035981

group: 5

ID Description GeneRatio BgRatio pvalue p.adjust qvalue
mmu05150 mmu05150 NA 4/26 51/6698 0.0000394 0.0017729 0.0010783
mmu04514 mmu04514 NA 5/26 154/6698 0.0002680 0.0043780 0.0026626
mmu05323 mmu05323 NA 4/26 85/6698 0.0002919 0.0043780 0.0026626
mmu05145 mmu05145 NA 4/26 128/6698 0.0013730 0.0125180 0.0076133
mmu04621 mmu04621 NA 3/26 58/6698 0.0013909 0.0125180 0.0076133
mmu05140 mmu05140 NA 3/26 65/6698 0.0019338 0.0145038 0.0088210
mmu05310 mmu05310 NA 2/26 24/6698 0.0037948 0.0243949 0.0148367
mmu04145 mmu04145 NA 4/26 179/6698 0.0046534 0.0261755 0.0159196
ID Description GeneRatio BgRatio pvalue p.adjust qvalue
GO:0002694 GO:0002694 regulation of leukocyte activation 12/50 446/23276 0.0000000 0.0000002 0.0000001
GO:0050900 GO:0050900 leukocyte migration 10/50 262/23276 0.0000000 0.0000002 0.0000001
GO:0002253 GO:0002253 activation of immune response 9/50 295/23276 0.0000000 0.0000009 0.0000006
GO:0030335 GO:0030335 positive regulation of cell migration 10/50 415/23276 0.0000000 0.0000012 0.0000007
GO:0001819 GO:0001819 positive regulation of cytokine production 7/50 357/23276 0.0000107 0.0002724 0.0001759
GO:0002274 GO:0002274 myeloid leukocyte activation 5/50 162/23276 0.0000253 0.0005347 0.0003453
GO:0043410 GO:0043410 positive regulation of MAPK cascade 7/50 434/23276 0.0000373 0.0007415 0.0004788
GO:0008360 GO:0008360 regulation of cell shape 4/50 121/23276 0.0001330 0.0020582 0.0013290
GO:0060627 GO:0060627 regulation of vesicle-mediated transport 6/50 405/23276 0.0002225 0.0032549 0.0021017
GO:0051085 GO:0051085 chaperone mediated protein folding requiring cofactor 2/50 12/23276 0.0002944 0.0040487 0.0026143
GO:0006887 GO:0006887 exocytosis 5/50 296/23276 0.0004265 0.0050837 0.0032826
GO:0006874 GO:0006874 cellular calcium ion homeostasis 5/50 358/23276 0.0010052 0.0095076 0.0061392

group: 6

ID Description GeneRatio BgRatio pvalue p.adjust qvalue
GO:0043252 GO:0043252 sodium-independent organic anion transport 3/36 28/23276 1.08e-05 0.0050942 0.0041872

group: 7

NULL

group: 8

ID Description GeneRatio BgRatio pvalue p.adjust qvalue
mmu04114 mmu04114 NA 5/28 114/6698 0.0000940 0.0039873 0.0032549
mmu04110 mmu04110 NA 5/28 128/6698 0.0001627 0.0039873 0.0032549
mmu00330 mmu00330 NA 3/28 54/6698 0.0014072 0.0229850 0.0187632
ID Description GeneRatio BgRatio pvalue p.adjust qvalue
GO:0002685 GO:0002685 regulation of leukocyte migration 7/79 155/23276 1.00e-06 0.0008678 0.0006487
GO:0007067 GO:0007067 mitotic nuclear division 10/79 399/23276 1.00e-06 0.0008678 0.0006487
GO:0050900 GO:0050900 leukocyte migration 8/79 262/23276 3.00e-06 0.0014303 0.0010692
GO:0007126 GO:0007126 meiotic nuclear division 6/79 156/23276 1.53e-05 0.0031920 0.0023861
GO:0000075 GO:0000075 cell cycle checkpoint 6/79 165/23276 2.10e-05 0.0031920 0.0023861
GO:0050920 GO:0050920 regulation of chemotaxis 6/79 181/23276 3.53e-05 0.0046279 0.0034595
GO:0006935 GO:0006935 chemotaxis 9/79 491/23276 4.27e-05 0.0048599 0.0036329
GO:0035239 GO:0035239 tube morphogenesis 8/79 393/23276 5.64e-05 0.0055256 0.0041305
GO:0044772 GO:0044772 mitotic cell cycle phase transition 7/79 295/23276 6.50e-05 0.0058725 0.0043898
GO:0048732 GO:0048732 gland development 8/79 408/23276 7.33e-05 0.0058725 0.0043898

group: 9

ID Description GeneRatio BgRatio pvalue p.adjust qvalue
mmu04973 mmu04973 NA 2/9 39/6698 0.0011591 0.03825 0.0353828

NULL

group: 10

ID Description GeneRatio BgRatio pvalue p.adjust qvalue
mmu05143 mmu05143 NA 2/5 32/6698 0.0002192 0.0013150 0.0004614
mmu05144 mmu05144 NA 2/5 47/6698 0.0004755 0.0014266 0.0005006
mmu00532 mmu00532 NA 1/5 22/6698 0.0163201 0.0288966 0.0101392
mmu00534 mmu00534 NA 1/5 26/6698 0.0192644 0.0288966 0.0101392
ID Description GeneRatio BgRatio pvalue p.adjust qvalue
GO:0048821 GO:0048821 erythrocyte development 3/13 32/23276 7e-07 0.0001344 7.81e-05

group: 11

ID Description GeneRatio BgRatio pvalue p.adjust qvalue
mmu04976 mmu04976 NA 3/5 71/6698 0.0000112 0.0000450 0.0000118
mmu04614 mmu04614 NA 1/5 19/6698 0.0141073 0.0282146 0.0074249

NULL

group: 13

ID Description GeneRatio BgRatio pvalue p.adjust qvalue
GO:0050900 GO:0050900 leukocyte migration 5/21 262/23276 0.0000031 0.0011583 0.0007223
GO:0010743 GO:0010743 regulation of macrophage derived foam cell differentiation 2/21 19/23276 0.0001313 0.0081437 0.0050780
GO:0002446 GO:0002446 neutrophil mediated immunity 2/21 24/23276 0.0002114 0.0096129 0.0059941

group: 14

NULL

group: 15

NULL

group: 16

ID Description GeneRatio BgRatio pvalue p.adjust qvalue
mmu00290 mmu00290 NA 1/4 11/6698 0.0065544 0.0491141 0.0140998
mmu00770 mmu00770 NA 1/4 15/6698 0.0089298 0.0491141 0.0140998

NULL

group: 22

ID Description GeneRatio BgRatio pvalue p.adjust qvalue
mmu05145 mmu05145 NA 2/3 128/6698 0.0010736 0.0257655 0.0079105
ID Description GeneRatio BgRatio pvalue p.adjust qvalue
GO:0072283 GO:0072283 metanephric renal vesicle morphogenesis 2/15 13/23276 0.0000301 0.0075758 0.0038011
GO:0060343 GO:0060343 trabecula formation 2/15 25/23276 0.0001153 0.0098772 0.0049558

R Session Info

(useful if replicating these results)

R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux stretch/sid

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  methods   stats     graphics  grDevices utils    
[8] datasets  base     

other attached packages:
 [1] hexbin_1.27.1              vsn_3.40.0                
 [3] DEGreport_1.5.0            quantreg_5.24             
 [5] SparseM_1.7                RUVSeq_1.6.2              
 [7] EDASeq_2.6.2               ShortRead_1.30.0          
 [9] GenomicAlignments_1.8.0    Rsamtools_1.24.0          
[11] Biostrings_2.40.0          XVector_0.12.0            
[13] BiocParallel_1.6.2         dplyr_0.4.3               
[15] cluster_2.0.4              org.Mm.eg.db_3.3.0        
[17] AnnotationDbi_1.34.2       clusterProfiler_3.0.2     
[19] DOSE_2.10.2                gridExtra_2.2.1           
[21] logging_0.7-103            tximport_1.0.2            
[23] DESeq2_1.12.2              SummarizedExperiment_1.2.2
[25] Biobase_2.32.0             GenomicRanges_1.24.0      
[27] GenomeInfoDb_1.8.1         IRanges_2.6.0             
[29] S4Vectors_0.10.0           BiocGenerics_0.18.0       
[31] pheatmap_1.0.8             CHBUtils_0.1              
[33] edgeR_3.14.0               limma_3.28.4              
[35] gplots_3.0.1               reshape_0.8.5             
[37] ggplot2_2.1.0              myRfunctions_0.1          
[39] knitr_1.13                 rmarkdown_0.9.6           
[41] BiocInstaller_1.22.2      

loaded via a namespace (and not attached):
 [1] colorspace_1.2-6       hwriter_1.3.2          qvalue_2.4.2          
 [4] MatrixModels_0.4-1     topGO_2.24.0           affyio_1.42.0         
 [7] splines_3.3.0          R.methodsS3_1.7.1      GOSemSim_1.30.2       
[10] DESeq_1.24.0           geneplotter_1.50.0     Formula_1.2-1         
[13] Nozzle.R1_1.1-1        annotate_1.50.0        GO.db_3.3.0           
[16] R.oo_1.20.0            graph_1.50.0           assertthat_0.1        
[19] Matrix_1.2-6           formatR_1.4            acepack_1.3-3.3       
[22] htmltools_0.3.5        tools_3.3.0            igraph_1.0.1          
[25] coda_0.18-1            gtable_0.2.0           affy_1.50.0           
[28] reshape2_1.4.1         DO.db_2.9              Rcpp_0.12.5           
[31] preprocessCore_1.34.0  gdata_2.17.0           rtracklayer_1.32.0    
[34] stringr_1.0.0          gtools_3.5.0           XML_3.98-1.4          
[37] zlibbioc_1.18.0        MASS_7.3-45            scales_0.4.0          
[40] aroma.light_3.2.0      RColorBrewer_1.1-2     yaml_2.1.13           
[43] biomaRt_2.28.0         rpart_4.1-10           latticeExtra_0.6-28   
[46] stringi_1.0-1          RSQLite_1.0.0          genefilter_1.54.2     
[49] GenomicFeatures_1.24.2 caTools_1.17.1         chron_2.3-47          
[52] matrixStats_0.50.2     bitops_1.0-6           evaluate_0.9          
[55] lattice_0.20-33        GSEABase_1.34.0        plyr_1.8.3            
[58] magrittr_1.5           R6_2.1.2               Hmisc_3.17-4          
[61] DBI_0.4-1              foreign_0.8-66         survival_2.39-4       
[64] RCurl_1.95-4.8         nnet_7.3-12            KernSmooth_2.23-15    
[67] locfit_1.5-9.1         grid_3.3.0             data.table_1.9.6      
[70] digest_0.6.9           xtable_1.8-2           tidyr_0.4.1           
[73] R.utils_2.3.0          munsell_0.4.3